sd_violin: Violin plots of CV per TMT_Set and LCMS_injection

In qzhang503/proteoQ: Processing and Informatic Analysis of Mass Spectrometrirc Data

Violin plots of CV per TMT_Set and LCMS_injection

Description

Violin plots of CV per TMT_Set and LCMS_injection

Usage

sd_violin(
  df = NULL,
  id = NULL,
  filepath = NULL,
  width = NULL,
  height = NULL,
  type = "log2_R",
  adjSD = FALSE,
  is_psm = FALSE,
  col_select = NULL,
  col_order = NULL,
  theme = NULL,
  ...
)

Arguments

df	The name of a primary data file. By default, it will be determined automatically after matching the types of data and analysis with an id among c("pep_seq", "pep_seq_mod", "prot_acc", "gene"). A primary file contains normalized peptide or protein data and is among c("Peptide.txt", "Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein.txt", "Protein_pVal.txt", "protein_impNA_pVal.txt"). For analyses require the fields of significance p-values, the df will be one of c("Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein_pVal.txt", "protein_impNA_pVal.txt").
id	Character string; one of pep_seq, pep_seq_mod, prot_acc and gene.
filepath	A file path to output results. By default, it will be determined automatically by the name of the calling function and the value of id in the call.
width	The width of a plot.
height	The height of a plot.
type	Character string; the type of data for SD calculations.
adjSD	Not currently used. If TRUE, adjust the standard deviation in relative to the width of ratio profiles.
is_psm	Logical; indicator if the data belong to a PSM table .
col_select	Character string to a column key in expt_smry.xlsx. At the NULL default, the column key of Select in expt_smry.xlsx will be used. In the case of no samples being specified under Select, the column key of Sample_ID will be used. The non-empty entries under the ascribing column will be used in indicated analysis.
col_order	Character string to a column key in expt_smry.xlsx. Numeric values under which will be used for the left-to-right arrangement of samples in graphic outputs or top-to-bottom arrangement in text outputs. At the NULL default, the column key Order will be used. If values under column Order are left blank, samples will be ordered by their names.
theme	A ggplot2 theme, i.e., theme_bw(), or a custom theme. At the NULL default, a system theme will be applied.
...	Additional parameters for plotting: ymax, the maximum y at a log2 scale. ybreaks, the breaks in y-axis at a log2 scale. width, the width of plot. height, the height of plot. flip_coord, logical; if TRUE, flip x and y axis.

qzhang503/proteoQ documentation built on March 16, 2024, 5:27 a.m.